SNP Technology Focuses on Terror Victims' IDs

Graphic: Courtesy of Orchid Biosciences  SNP-based identifications are possible with fragments one-fourth the size needed for other methods. A well-lit, chrome-and-steel room hums as a robot uses multiple arms to carry 384-well plates from their platforms into readers, where an "SNPscope"--which has the capacity to read just a few pixels of fluorescence--captures data from the entire plate in six minutes and automatically transfers it to computer screens. A half-dozen researchers and ana

By | October 14, 2002

Graphic: Courtesy of Orchid Biosciences
 SNP-based identifications are possible with fragments one-fourth the size needed for other methods.

A well-lit, chrome-and-steel room hums as a robot uses multiple arms to carry 384-well plates from their platforms into readers, where an "SNPscope"--which has the capacity to read just a few pixels of fluorescence--captures data from the entire plate in six minutes and automatically transfers it to computer screens. A half-dozen researchers and analysts, led by Robert Giles, executive director of the identity genomics group at Orchid Cellmark's Dallas, Texas, laboratory, pore over the data. Their mission: Increase the odds of identifying remains of people killed in the Sept. 11, 2001 terrorist attack that brought down the World Trade Center towers in New York.

Orchid Cellmark, a business unit of Orchid BioSciences in Princeton, NJ, joined the massive forensics effort officially in August, after months of tests and trials passed muster with the review board overseeing the work managed by the New York City Medical Examiner's (ME) Office. That office's director of forensic biology, Robert Shaler, called Orchid Cellmark executive director Mark Stolorow last December, after analysis of more than half of the 20,000 forensic samples from Ground Zero resulted in partial, incomplete, or no DNA profiles.

New York officials are hoping that state-of-the-art single nucleotide polymorphism (SNP) technology will be able to identify samples--some as small as a fingertip--that other forensic methods cannot. Those samples include small fragments of tissue, bone, or body parts stored in deep freezers in 16 portable refrigerator trucks outside the ME's office, Stolorow says. "Their conditions of high heat, humidity, bacteria, and pressure caused DNA to begin to break down in a way not characteristic of most crime scenes," he adds.

The SNP analyses will be conducted in two stages. The first will be to test the approximately 6,000 "reference" samples--a victim's toothbrush or hairbrush, for instance, or DNA from a cheek swab of a victim's relative--and build a database. Then, the researchers will analyze the data from the Ground Zero samples and make comparisons.

SNP analysis has two major advantages over some other DNA forensics methods, such as short tandem repeats, Stolorow explains. Because SNPs are sequence polymorphisms and not length polymorphisms, "We're looking at differences of only one base pair between forms in the population, and we have reconfigured our SNP panel for forensic testing to requiring no more than 60 to 80 nucleotides for the remaining fragments of DNA. That, literally, is just above the level of not having any remaining DNA at all." Also, SNP technology works with samples that are 120 picograms or smaller, he says.

The Orchid Cellmark work is just one of several efforts involved in the overall project.1 Others include the ME's office (tissue analysis), Springfield, Va.-based Bode Technology Group (bone analysis), and Celera Genomics Group of Rockville, Md. (mitochondrial DNA analysis).

Stolorow says that, with the Dallas lab processing about 4,000 samples a month with the Orchid BioSciences SNPstream® ultrahigh-throughput technology, the SNP work could be done by the end of this year. If the work is as successful as he and others are hoping for, it could have a major impact on forensics. The technology, he adds, can be used with lab instruments already in place, so the transfer to facilities worldwide would be fairly straightforward.

As Stolorow sums it up, "It is a very interesting marriage between the latest advances in technology and the critically challenging need in the forensics community that 12 months ago did not have this capability."

Larry Hand can be contacted at lhand@the-scientist.com.

1. K.A. Miller, "Identifying those remembered," The Scientist, 16[12]:40-2, June 10, 2002.
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